File sizes are an issue and xml won’t help. The file formats are wierd (fasta?) but they are at least kinda standard.

There are groups dedicated to organizing/ annotating genes. They’re quite organized and have highly structured databases.

http://gmod.org/wiki/Introduction_to_Chado

A lot of the model orgainism species have gotten together to make thinks more uniform.

https://www.alliancegenome.org/

Also most people in this field are using free software.